Composed of NCDA members, the NCD Alliance General Assembly is the organisation's supreme decision-making body. The GA meets every two years, and elects NCDA's President and Board.  It can amend the constitution and receives and adopts the Alliance's reports and financial accounts.

There are four founding members of the NCDA: International Diabetes Federation, World Heart Federation, Union for International Cancer Control and The Union. Founding members can vote at the General Assembly and can nominate individuals for election as NCDA President and Board members. In addition, founding members are entitled to a permanent seat on the Board.

Full NCDA members are entitled to attend and vote at the GA and can nominate individuals for President / Board. Associate members can attend the GA as observers (but not vote) and can nominate individuals for the Board (not for President).

The first NCDA General Assembly was held on 22 May 2017, in Geneva.